[gmx-users] Problems about sigma & epsilon to C6 & C12

[james zhang]

You should get identical plots. I think rule 1 and rule 3 are equivalent.

On 7/16/07, Janne Hirvi <janne.hirvi at joensuu.fi> wrote:
>
> Hello!
>
> Could you please help me to understand solution as well? I just plotted
> these
> functions so that I combined sigma and epsilon values using rule 3
>
> sigma(ij)=(sigma(i)*sigma(j))^(1/2)
> epsilon(ij)=(epsilon(i)*epsilon(j))^(1/2)
>
> and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^12)
> values
> using rule 1
>
> C6(ij)=(C6(i)*C6(j))^(1/2)
> C12(ij)=(C12(i)*C12(j))^(1/2)
>
> and got identical plots. What I have missed?
>
> Janne
>
> >
> > My problem has solved. Finally I realized that my calculation is wrong.
> > Thank you so much!
> >
> > On 7/15/07, james zhang <james.zhangj at gmail.com> wrote:
> > >
> > > From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you
> > > convert the parameters.
> > > I am sorry. What's the different between rule 1 and 3?
> > > I think C6/C12 are used in rule 1 and sigma/epsilon are used in rule
> 3.
> > > But if you convert sigma/epsilon to C6/C12, these two should be
> > equivalent.
> > > I am confused. Can I convert sigma/epsilon to C6/C12 if I want to use
> gmx
> > > force field instead of OPLS ?
> > > Thanks.
> > >
> > > On 7/15/07, David van der Spoel < spoel at xray.bmc.uu.se> wrote:
> > > >
> > > > james zhang wrote:
> > > > > I used rule 3 for ffopls rule 1 for ffgmx.
> > > > >
> > > > please read the manual.these combination rules are not equivalent.
> > > >
> > > > there is also combination rule 2, see 5.3.3
> > > > --
> > > > David.
> > > >
> ________________________________________________________________________
> > > >
> > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > > > phone:  46 18 471 4205          fax: 46 18 511 755
> > > > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > > >
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-- 
Sincerely yours,
James Jianzhang
Department of Mechanical and Chemical Engineering
North Carolina Agricultural and Technical State University
1601 East Market Street
Greensboro, NC 27411
jzhang at ncat.edu or james.zhangj at gmail.com
http://www.ncat.edu/~jzhang
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